Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 191 of 206
Found at i:57926210 original size:3 final size:3
Alignment explanation
Indices: 57926202--57926246 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
57926192 TAATAGTATC
* *
57926202 AAT AAT AAT -AT GAGT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
57926247 GAAAATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 33 0.92
4 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57926245 original size:15 final size:15
Alignment explanation
Indices: 57926191--57926246 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
57926181 ATAACTAAAT
* *
57926191 ATAATAGTATCAATA
1 ATAATAATAACAATA
*
57926206 ATAATATGAGTAATAATA
1 ATAATA--A-TAACAATA
57926224 ATAATAATAACAATA
1 ATAATAATAACAATA
57926239 ATAATAAT
1 ATAATAAT
57926247 GAAAATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.62
16 1 0.03
18 12 0.35
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (15 bp):
ATAATAATAACAATA
Found at i:57929009 original size:3 final size:3
Alignment explanation
Indices: 57929001--57929026 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57928991 TTCACTTCCC
57929001 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
57929027 GGTTCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:57931651 original size:9 final size:9
Alignment explanation
Indices: 57931579--57931655 Score: 75
Period size: 9 Copynumber: 8.4 Consensus size: 9
57931569 TTTGGTTAAA
*
57931579 AATTACTCG
1 AATTACCCG
*
57931588 AATTACTCG
1 AATTACCCG
57931597 AATTACCCG
1 AATTACCCG
*
57931606 AATTAACCG
1 AATTACCCG
* *
57931615 AATTAACCA
1 AATTACCCG
57931624 AATTA-CCG
1 AATTACCCG
*
57931632 AAAAATACCCG
1 --AATTACCCG
57931643 AATTACCCG
1 AATTACCCG
57931652 AATT
1 AATT
57931656 TTTTTATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
8 2 0.03
9 50 0.85
10 4 0.07
11 3 0.05
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:57937319 original size:13 final size:13
Alignment explanation
Indices: 57937292--57937324 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
57937282 TAAGGACTAC
57937292 AAAAGTGAAATGT
1 AAAAGTGAAATGT
57937305 AAAATGTGAAA-GT
1 AAAA-GTGAAATGT
57937318 AAAAGTG
1 AAAAGTG
57937325 TACGTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 10 0.53
14 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (13 bp):
AAAAGTGAAATGT
Found at i:57938331 original size:39 final size:39
Alignment explanation
Indices: 57938272--57938351 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
57938262 GCCGTTATAG
* *
57938272 AACATGACCTTTAACGGCGCTTTTCCCACAAACGCCACT
1 AACATGACCTTTAACAGCGCTTTCCCCACAAACGCCACT
* *
57938311 AACATGACCTTTAGCAGCGCTTTCCCCACAAACGCCGCT
1 AACATGACCTTTAACAGCGCTTTCCCCACAAACGCCACT
57938350 AA
1 AA
57938352 AGAACATGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (39 bp):
AACATGACCTTTAACAGCGCTTTCCCCACAAACGCCACT
Found at i:57938356 original size:82 final size:81
Alignment explanation
Indices: 57938176--57938384 Score: 247
Period size: 82 Copynumber: 2.5 Consensus size: 81
57938166 GTGGAAAAAT
* * * * **
57938176 GCCGCTATAGAACATGACATCTAGCGATGCTTTTCCCACAAACGCTGCTAAAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTA-CGACGCTTTTCCCACAAACGC--C--ACTAACATGACCTTT
* *
57938241 AGCGGCGCTTACCCCACAAAT
61 AGCAGCGCTTACCCCACAAAC
* * *
57938262 GCCGTTATAGAACATGACCTTTAACGGCGCTTTTCCCACAAACGCCACTAACATGACCTTTAGCA
1 GCCGCTAAAGAACATGACCTTT-ACGACGCTTTTCCCACAAACGCCACTAACATGACCTTTAGCA
*
57938327 GCGCTTTCCCCACAAAC
65 GCGCTTACCCCACAAAC
*
57938344 GCCGCTAAAGAACATGACCTTTACGATGCTTTTCCCACAAA
1 GCCGCTAAAGAACATGACCTTTACGACGCTTTTCCCACAAA
57938385 TGACGCTAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
81 17 0.16
82 51 0.47
84 1 0.01
86 38 0.35
87 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (81 bp):
GCCGCTAAAGAACATGACCTTTACGACGCTTTTCCCACAAACGCCACTAACATGACCTTTAGCAG
CGCTTACCCCACAAAC
Found at i:57938419 original size:43 final size:43
Alignment explanation
Indices: 57938172--57938420 Score: 265
Period size: 43 Copynumber: 5.9 Consensus size: 43
57938162 TTATGTGGAA
* * * **
57938172 AAATGCCGCTATAGAACATGACATCTAGCGATGCTTTTCCCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * **
57938215 AAACGCTGCTAAAGAACATGACCTTTAGCGGCGCTTACCCCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
57938258 AAATGCCGTTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
57938301 AAACGCCACT----AACATGACCTTTAGCAGCGCTTTCCCCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* **
57938340 AAACGCCGCTAAAGAACATGACCTTTA-CGATGCTTTTCCCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
57938382 AAATGACGCTAAAGAACATGACTTTTAGCGGTGCTTTTC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTC
57938421 TTAAAAACGC
Statistics
Matches: 170, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
39 35 0.21
42 35 0.21
43 100 0.59
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:57938452 original size:43 final size:43
Alignment explanation
Indices: 57938204--57938543 Score: 152
Period size: 43 Copynumber: 8.0 Consensus size: 43
57938194 ATCTAGCGAT
* * ** **
57938204 GCTTTTCCCACAAACGCTGCTAAAGAACATGACCTTTAGCGGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
** * * * * ** ** *
57938247 GCTTACCCCACAAATGCCGTTATAGAACATGACCTTTAACGGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
* * ** *
57938290 GCTTTTCCCACAAACGCCACT-AA---CATGACCTTTAGCAGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
* * ** ** **
57938329 GCTTTCCCCACAAACGCCGCTAAAGAACATGACCTTTA-CGAT
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
* * * ** * *
57938371 GCTTTTCCCACAAATGACGCTAAAGAACATG-ACTTTTAGCGGT
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTC-TTTAGCGGC
** * * *
57938414 GCTTTTCTTAAAAACGCTGCTAAAGGTCATTTTCTTTAGTGGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
* * *
57938457 GCTTTTCCCAATAACGCCGCTAAATGTCATGTTCTTTAGCAGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
* *** * * * *
57938500 GTTTTTAGTAAAAGCGCCGCTAAAAGTCTTGTTCTTTGGCGGC
1 GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
57938543 G
1 G
57938544 TTTGTGGAAA
Statistics
Matches: 235, Mismatches: 55, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
39 33 0.14
40 2 0.01
41 1 0.00
42 34 0.14
43 164 0.70
44 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (43 bp):
GCTTTTCCCAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGC
Found at i:57942299 original size:21 final size:22
Alignment explanation
Indices: 57942255--57942309 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
57942245 TGAAATTTAT
57942255 TTTTAGGGTTTAAGGTTAATAG
1 TTTTAGGGTTTAAGGTTAATAG
* *
57942277 -TTTAGGGTTTATGATTTAA-AG
1 TTTTAGGGTTTAAG-GTTAATAG
*
57942298 TTTTAGGATTTA
1 TTTTAGGGTTTA
57942310 GAGTTTTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (22 bp):
TTTTAGGGTTTAAGGTTAATAG
Found at i:57942307 original size:15 final size:15
Alignment explanation
Indices: 57942284--57942325 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
57942274 TAGTTTAGGG
*
57942284 TTTATGATTTAAAGT
1 TTTAGGATTTAAAGT
*
57942299 TTTAGGATTTAGAGT
1 TTTAGGATTTAAAGT
57942314 TTTGAGG-TTTAA
1 TTT-AGGATTTAA
57942326 GGATAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (15 bp):
TTTAGGATTTAAAGT
Found at i:57946883 original size:18 final size:19
Alignment explanation
Indices: 57946848--57946885 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
57946838 TATTAAATTA
* *
57946848 TTTCAATAATATTTTTTAT
1 TTTCAATAACATTATTTAT
57946867 TTTCAATAACA-TATTTAT
1 TTTCAATAACATTATTTAT
57946885 T
1 T
57946886 AAAAAGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTCAATAACATTATTTAT
Found at i:57951958 original size:42 final size:42
Alignment explanation
Indices: 57951895--57951991 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
57951885 GTTAATATTT
* *
57951895 TATTAATTTA-ATATTAATATGAGATATTAAACTTAATTTAA
1 TATTTATTTAGATATTAATATGAGATAATAAACTTAATTTAA
* *
57951936 TATTTATTTAGATATTACTATGAGATAATAAATTTAATTTAA
1 TATTTATTTAGATATTAATATGAGATAATAAACTTAATTTAA
*
57951978 TATTTATCTAGATA
1 TATTTATTTAGATA
57951992 ATATTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 9 0.18
42 41 0.82
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (42 bp):
TATTTATTTAGATATTAATATGAGATAATAAACTTAATTTAA
Found at i:57951980 original size:103 final size:103
Alignment explanation
Indices: 57951816--57952015 Score: 287
Period size: 103 Copynumber: 1.9 Consensus size: 103
57951806 ATGAATTTAT
** *
57951816 TATTAAATTAAATTAAATATTTATTTGAATATTAATAAGAGATGTTATATTAAATTAAATATTTA
1 TATTAAATTAAATTAAATATTTATTTGAATATTAATAAGAGATAATAAATTAAATTAAATATTTA
*
57951881 TCTAGTTAATATTTTATTAATTTAATATTAATATGAGA
66 TCTAGATAATATTTTATTAATTTAATATTAATATGAGA
* * * * *
57951919 TATTAAACTT-AATTTAATATTTATTT-AGATATTACTATGAGATAATAAATTTAATTTAATATT
1 TATTAAA-TTAAATTAAATATTTATTTGA-ATATTAATAAGAGATAATAAATTAAATTAAATATT
57951982 TATCTAGATAATATTTTATTAATTTAATATTAAT
64 TATCTAGATAATATTTTATTAATTTAATATTAAT
57952016 GTGATTAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 1 0.01
103 83 0.97
104 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (103 bp):
TATTAAATTAAATTAAATATTTATTTGAATATTAATAAGAGATAATAAATTAAATTAAATATTTA
TCTAGATAATATTTTATTAATTTAATATTAATATGAGA
Found at i:57960810 original size:7 final size:7
Alignment explanation
Indices: 57960800--57960844 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
57960790 TTGGGTTATT
57960800 GGTTTAG
1 GGTTTAG
57960807 GGTTTAG
1 GGTTTAG
57960814 GG-TTAG
1 GGTTTAG
*
57960820 GGTTTTG
1 GGTTTAG
57960827 GTGTTTTAG
1 G-G-TTTAG
57960836 GGTTTAG
1 GGTTTAG
57960843 GG
1 GG
57960845 CTTAAGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.18
7 20 0.61
8 2 0.06
9 5 0.15
ACGTcount: A:0.11, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:57961388 original size:11 final size:11
Alignment explanation
Indices: 57961374--57961405 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
57961364 TTTAAATAGA
57961374 AATTTGAGAGG
1 AATTTGAGAGG
57961385 AATTTGAGAGG
1 AATTTGAGAGG
57961396 AATTTGAGAG
1 AATTTGAGAG
57961406 AATATTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:57963417 original size:17 final size:17
Alignment explanation
Indices: 57963388--57963512 Score: 98
Period size: 16 Copynumber: 7.4 Consensus size: 17
57963378 ACACAATAAT
57963388 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
57963405 AGATTTTTG-AAACACGAA
1 A-ATTTTTGAAAACACG-A
57963423 AATTTTTTGAAAACACGGA
1 AA-TTTTTGAAAACAC-GA
* *
57963442 AATTTTCG-ATACACGA
1 AATTTTTGAAAACACGA
***
57963458 AATTTTT-TTGACACGA
1 AATTTTTGAAAACACGA
*
57963474 AA-ATTTGAAAACACGA
1 AATTTTTGAAAACACGA
* * *
57963490 AAATTTCGAAAACATG-
1 AATTTTTGAAAACACGA
57963506 AATTTTT
1 AATTTTT
57963513 TCCTTTTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 17
0.74 0.12 0.15
Matches are distributed among these distances:
15 3 0.03
16 29 0.34
17 24 0.28
18 20 0.23
19 9 0.10
20 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:57963435 original size:36 final size:35
Alignment explanation
Indices: 57963372--57963495 Score: 123
Period size: 36 Copynumber: 3.5 Consensus size: 35
57963362 ATACGAGAAA
57963372 TTTGAAACAC-AATAATAATTTTTGAAAACACGAAGATT
1 TTTGAAACACGAA-AAT--TTTTTGAAAACACGAA-ATT
57963410 TTTGAAACACGAAAATTTTTTGAAAACACGGAAATT
1 TTTGAAACACGAAAATTTTTTGAAAACAC-GAAATT
* * * *
57963446 TTCGATACACGAAATTTTTTTG---ACACGAAA-A
1 TTTGAAACACGAAAATTTTTTGAAAACACGAAATT
57963477 TTTGAAAACACGAAAATTT
1 TTTG-AAACACGAAAATTT
57963496 CGAAAACATG
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.04
32 16 0.21
33 4 0.05
36 35 0.46
37 3 0.04
38 13 0.17
39 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTGAAACACGAAAATTTTTTGAAAACACGAAATT
Found at i:57963648 original size:44 final size:42
Alignment explanation
Indices: 57963600--57963681 Score: 128
Period size: 44 Copynumber: 1.9 Consensus size: 42
57963590 AAACACGAAA
57963600 AAAATTTTGAAACACGGGAATTTTTTTGAAAACACAAAAACACG
1 AAAATTTTGAAACACGGGAA-TTTTTTG-AAACACAAAAACACG
* *
57963644 AAAATTTTTAAACACGGGAATTTTTTGAAACACGAAAA
1 AAAATTTTGAAACACGGGAATTTTTTGAAACACAAAAA
57963682 TTTTTGAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 10 0.28
43 7 0.19
44 19 0.53
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (42 bp):
AAAATTTTGAAACACGGGAATTTTTTGAAACACAAAAACACG
Found at i:57963675 original size:34 final size:35
Alignment explanation
Indices: 57963637--57963704 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
57963627 GAAAACACAA
57963637 AAACACGAAAATTTTT-AAACACGG-GAATTTTTTG
1 AAACACGAAAATTTTTGAAACA-GGAGAATTTTTTG
57963671 AAACACGAAAATTTTTGAAACAGGAGAATTTTTT
1 AAACACGAAAATTTTTGAAACAGGAGAATTTTTT
57963705 TTTTTGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 18 0.56
35 14 0.44
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (35 bp):
AAACACGAAAATTTTTGAAACAGGAGAATTTTTTG
Found at i:57963685 original size:17 final size:17
Alignment explanation
Indices: 57963637--57963703 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
57963627 GAAAACACAA
57963637 AAACACGAAAATTTTT-
1 AAACACGAAAATTTTTG
* *
57963653 AAACACGGGAATTTTTTG
1 AAACAC-GAAAATTTTTG
57963671 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
* *
57963688 AAACAGGAGAATTTTT
1 AAACACGAAAATTTTT
57963704 TTTTTTGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
16 6 0.14
17 31 0.72
18 6 0.14
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:57963751 original size:19 final size:19
Alignment explanation
Indices: 57963727--57963763 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
57963717 CAAAAACATG
57963727 AAAA-TTTTGAAAACACGAA
1 AAAATTTTTG-AAACACGAA
57963746 AAAATTTTTGAAACACGA
1 AAAATTTTTGAAACACGA
57963764 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAATTTTTGAAACACGAA
Found at i:57963796 original size:16 final size:17
Alignment explanation
Indices: 57963774--57963815 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
57963764 TTTTTTTTAA
57963774 AAAAACACGGAAA-TTT
1 AAAAACACGGAAACTTT
* *
57963790 TAAAACATGGAAACTTT
1 AAAAACACGGAAACTTT
57963807 AAAAACACG
1 AAAAACACG
57963816 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAACACGGAAACTTT
Found at i:57963856 original size:147 final size:144
Alignment explanation
Indices: 57963554--57963848 Score: 368
Period size: 147 Copynumber: 2.1 Consensus size: 144
57963544 AACATGAGAA
*
57963554 TTTTTTTTTGAAAACACGAAAACATGAAAATTTTGAAAACACGAAAAAAATTTTGAAACACGGGA
1 TTTTTTTTTGAAAACACAAAAACATGAAAATTTTGAAAACACGAAAAAAATTTTGAAACAC-GGA
* ** **
57963619 ATTTTTTTGAAAACACAAAAACACGAAAATTTTTAAACACGGGAATTTTTTGAAACACGAAAATT
65 ATTTTTTT--AAACACAAAAACACGAAAATTTTAAAACACGGGAAACTTTAAAAACACGAAAATT
* **
57963684 TTTGAAACAGGAGAATT
128 TTTAAAACACAAGAATT
*
57963701 TTTTTTTTTGAAAACACAAAAACATGAAAATTTTGAAAACACGAAAAAATTTTTGAAACAC-G-A
1 TTTTTTTTTGAAAACACAAAAACATGAAAATTTTGAAAACACGAAAAAAATTTTGAAACACGGAA
* * * **
57963764 TTTTTTT-TA-A-AAAAACACGGAAATTTTAAAACA-TGGAAACTTTAAAAACACGAATTTTTTT
66 TTTTTTTAAACACAAAAACACGAAAATTTTAAAACACGGGAAACTTTAAAAACACGAAAATTTTT
*
57963825 AAAACACAAGATTT
131 AAAACACAAGAATT
57963839 TTATTTTTTT
1 TT-TTTTTTT
57963849 ATTTTTTTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
138 33 0.25
139 28 0.21
140 1 0.01
141 1 0.01
144 8 0.06
145 1 0.01
147 59 0.45
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (144 bp):
TTTTTTTTTGAAAACACAAAAACATGAAAATTTTGAAAACACGAAAAAAATTTTGAAACACGGAA
TTTTTTTAAACACAAAAACACGAAAATTTTAAAACACGGGAAACTTTAAAAACACGAAAATTTTT
AAAACACAAGAATT
Found at i:57964692 original size:13 final size:12
Alignment explanation
Indices: 57964669--57964728 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
57964659 CTGTTGTTTT
57964669 TTTTTTCCTCTTTC
1 TTTTTT-CTC-TTC
57964683 TTTTTTCTC-TC
1 TTTTTTCTCTTC
57964694 -TTTTTCTTCTTC
1 TTTTTTC-TCTTC
57964706 -TTTTTCT-TTC
1 TTTTTTCTCTTC
57964716 TTTTTTC-CTTC
1 TTTTTTCTCTTC
57964727 TT
1 TT
57964729 CTTCTTCGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.21
11 16 0.38
12 8 0.19
13 3 0.07
14 6 0.14
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTCTCTTC
Found at i:57964704 original size:24 final size:22
Alignment explanation
Indices: 57964670--57964731 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 22
57964660 TGTTGTTTTT
57964670 TTTTTCCTCTTTCTTTTTTCTCTC
1 TTTTTCCTC-TTC-TTTTTCTCTC
* *
57964694 TTTTTCTTCTTCTTTTTCTTTC
1 TTTTTCCTCTTCTTTTTCTCTC
57964716 TTTTTTCCTTCTTCTT
1 -TTTTTCC-TCTTCTT
57964732 CTTCGGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 9 0.27
23 9 0.27
24 15 0.45
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTCCTCTTCTTTTTCTCTC
Found at i:57965326 original size:30 final size:29
Alignment explanation
Indices: 57965292--57965417 Score: 126
Period size: 30 Copynumber: 4.2 Consensus size: 29
57965282 AAATATGGGC
*
57965292 CAAAATGTAATTTCTTGAAAGTTTAGGGGT
1 CAAAATGTAATTT-TAGAAAGTTTAGGGGT
* * * *
57965322 CAAAATGTAATTTAAAAAATTTTAGGGTT
1 CAAAATGTAATTTTAGAAAGTTTAGGGGT
** * * *
57965351 TGAACTGTAATTTTGAGAAATTTTAGGAGT
1 CAAAATGTAATTTT-AGAAAGTTTAGGGGT
*
57965381 CAAAATGCAATTTTAGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTAG-AAAGTTTAGGGGT
57965411 CAAAATG
1 CAAAATG
57965418 CAAAAAAAAT
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.30
30 53 0.70
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAGTTTAGGGGT
Found at i:57980221 original size:11 final size:11
Alignment explanation
Indices: 57980200--57980233 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
57980190 AATATCACAA
57980200 AAAACTAAGTTG
1 AAAA-TAAGTTG
57980212 AAAATAAGTTG
1 AAAATAAGTTG
57980223 AAAATAAGTTG
1 AAAATAAGTTG
57980234 TTTGATCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (11 bp):
AAAATAAGTTG
Found at i:57980951 original size:42 final size:42
Alignment explanation
Indices: 57980904--57980988 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
57980894 CGGTATGCAT
57980904 CAATCACTCTACCACTAGCACTAAAAGCAGATTTTGAAGCCA
1 CAATCACTCTACCACTAGCACTAAAAGCAGATTTTGAAGCCA
57980946 CAATCACTCTACCACTAGCACTAAAAGCAGATTTTGAAGCCA
1 CAATCACTCTACCACTAGCACTAAAAGCAGATTTTGAAGCCA
57980988 C
1 C
57980989 TGTGTTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (42 bp):
CAATCACTCTACCACTAGCACTAAAAGCAGATTTTGAAGCCA
Found at i:57987838 original size:22 final size:22
Alignment explanation
Indices: 57987810--57987852 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
57987800 TTTTATTTTC
**
57987810 AAAAAAAAAAAGTTAAAAAGAT
1 AAAAAAAAAAAGAAAAAAAGAT
57987832 AAAAAAAAAAAGAAAAAAAGA
1 AAAAAAAAAAAGAAAAAAAGA
57987853 AGAACCCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAAAAAGAT
Found at i:57993371 original size:18 final size:17
Alignment explanation
Indices: 57993345--57993380 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
57993335 TCTTTTAGGA
*
57993345 ATTATAATGATATAAATT
1 ATTAAAATGATA-AAATT
57993363 ATTAAAATGATAAAATT
1 ATTAAAATGATAAAATT
57993380 A
1 A
57993381 CATTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
ATTAAAATGATAAAATT
Found at i:57993781 original size:2 final size:2
Alignment explanation
Indices: 57993774--57993803 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57993764 GTGACAATCC
57993774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57993804 GTAGCTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57996935 original size:31 final size:31
Alignment explanation
Indices: 57996877--57996935 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
57996867 GGTGCAGTTA
**
57996877 TATACATGAAACTTAGATTGTGGTTCAACTG
1 TATACATGAAACTTAGATTGTAATTCAACTG
*
57996908 TATACATGAAACCTTA-ATTTTAATTCAA
1 TATACATGAAA-CTTAGATTGTAATTCAA
57996936 TCATAATCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (31 bp):
TATACATGAAACTTAGATTGTAATTCAACTG
Found at i:57997765 original size:93 final size:91
Alignment explanation
Indices: 57997585--57997798 Score: 260
Period size: 93 Copynumber: 2.4 Consensus size: 91
57997575 GTAAAAAGTT
* * * *
57997585 CTCAAATTTTTTC-AAAAAAAAGCAATTAAGCCCCTCTTTTTTTTTGCACTTAATTTAGCACTTG
1 CTCAAAATTTTTCAAAAAAAAAGCAATTAAGCCCCCCTTTTTTTTTGCACTCAATTGAGCACTTG
*
57997649 AACTTTCAAAATACATCAAAAAGACC
66 AACTTTCAAAATACATAAAAAAGACC
* * * *
57997675 CTCAAACTTCTTCAAAAAAAGAAGCAATTAAGCCCCAGCCTTTTTTTTT-CACTCAATTGGGTAC
1 CTCAAAATTTTTCAAAAAAA-AAGCAATTAAGCCCC--CCTTTTTTTTTGCACTCAATTGAGCAC
*
57997739 TTGAACTTTCAAAATGA-ATAAAAAAGACT
63 TTGAACTTTCAAAAT-ACATAAAAAAGACC
57997768 CTCAAAATTTTTC--AAAAAAA-CAATTAAGCCC
1 CTCAAAATTTTTCAAAAAAAAAGCAATTAAGCCC
57997799 TTGCTCTAGT
Statistics
Matches: 108, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
89 11 0.10
90 13 0.12
91 11 0.10
92 15 0.14
93 47 0.44
94 11 0.10
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (91 bp):
CTCAAAATTTTTCAAAAAAAAAGCAATTAAGCCCCCCTTTTTTTTTGCACTCAATTGAGCACTTG
AACTTTCAAAATACATAAAAAAGACC
Found at i:57997836 original size:7 final size:7
Alignment explanation
Indices: 57997812--57997848 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
57997802 CTCTAGTTAA
57997812 AAATTAG
1 AAATTAG
*
57997819 AAA--AA
1 AAATTAG
57997824 AAATTAG
1 AAATTAG
57997831 AAATTAG
1 AAATTAG
57997838 AAATTAG
1 AAATTAG
57997845 AAAT
1 AAAT
57997849 AATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
5 4 0.15
7 22 0.85
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (7 bp):
AAATTAG
Found at i:57997843 original size:14 final size:13
Alignment explanation
Indices: 57997809--57997856 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
57997799 TTGCTCTAGT
57997809 TAAAAATTAGAAA
1 TAAAAATTAGAAA
57997822 -AAAAATTAGAAA
1 TAAAAATTAGAAA
*
57997834 TTAGAAATTAGAAA
1 -TAAAAATTAGAAA
57997848 TAATAAATT
1 TAA-AAATT
57997857 TTAGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 12 0.40
13 2 0.07
14 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (13 bp):
TAAAAATTAGAAA
Found at i:57997903 original size:25 final size:24
Alignment explanation
Indices: 57997868--57997950 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
57997858 TAGAAAAATG
*
57997868 ATTAAATTTTAATAAAAATATAAAA
1 ATTAAAATTTAATAAAAAT-TAAAA
*
57997893 ATTAAAATTTATTAAAAATTACAAA
1 ATTAAAATTTAATAAAAATTA-AAA
* *
57997918 A-AAAATATTTTATAAAAATCGTAAAA
1 ATTAAA-ATTTAATAAAAAT--TAAAA
*
57997944 AATAAAA
1 ATTAAAA
57997951 AAAATTGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
24 5 0.11
25 32 0.68
26 5 0.11
27 5 0.11
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (24 bp):
ATTAAAATTTAATAAAAATTAAAA
Found at i:57997910 original size:26 final size:25
Alignment explanation
Indices: 57997868--57997936 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
57997858 TAGAAAAATG
* *
57997868 ATTAAATTTTAATAAAAATATAAAA
1 ATTAAAATTTAATAAAAATACAAAA
*
57997893 ATTAAAATTTATTAAAAATTACAAAA
1 ATTAAAATTTAATAAAAA-TACAAAA
*
57997919 A--AAATATTTTATAAAAAT
1 ATTAAA-ATTTAATAAAAAT
57997937 CGTAAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 4 0.11
25 26 0.70
26 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (25 bp):
ATTAAAATTTAATAAAAATACAAAA
Found at i:57998165 original size:9 final size:9
Alignment explanation
Indices: 57998151--57998410 Score: 69
Period size: 9 Copynumber: 28.2 Consensus size: 9
57998141 CTTCTTTTGG
57998151 TATAATTTT
1 TATAATTTT
57998160 TATAATTTTT
1 TATAA-TTTT
*
57998170 TATGAA-ATT
1 TAT-AATTTT
57998179 TAT-ATTTCT
1 TATAATTT-T
57998188 T-TACATTTT
1 TATA-ATTTT
57998197 GTATAATTTTCT
1 -TATAA-TTT-T
* *
57998209 TATGA-CTT
1 TATAATTTT
*
57998217 TATAAAATTT
1 TAT-AATTTT
57998227 TATAATTTT
1 TATAATTTT
* *
57998236 TTTATATTTC
1 TATA-ATTTT
57998246 TAT-ATATTT
1 TATAAT-TTT
57998255 TATAATTTT
1 TATAATTTT
57998264 T-TACGATTTT
1 TATA--ATTTT
*
57998274 TATAAAATTT
1 TAT-AATTTT
**
57998284 TGCAACTTTT
1 TATAA-TTTT
*
57998294 TAT-TTTTT
1 TATAATTTT
*
57998302 TACAATTTT
1 TATAATTTT
*
57998311 TAT-TTTTT
1 TATAATTTT
*
57998319 TCTAATTTT
1 TATAATTTT
* *
57998328 AATAAATTT
1 TATAATTTT
57998337 T-TAATATTT
1 TATAAT-TTT
* *
57998346 GA-ATTTTT
1 TATAATTTT
57998354 TATTAAATTTT
1 TA-T-AATTTT
* *
57998365 AATAATATT
1 TATAATTTT
57998374 TAT-ATCTTT
1 TATAAT-TTT
*
57998383 TATTGA-TTT
1 TA-TAATTTT
*
57998392 TA-AGTTTT
1 TATAATTTT
57998400 TATAATTTT
1 TATAATTTT
57998409 TA
1 TA
57998411 ATAAAAGCAG
Statistics
Matches: 179, Mismatches: 40, Indels: 64
0.63 0.14 0.23
Matches are distributed among these distances:
7 1 0.01
8 36 0.20
9 78 0.44
10 43 0.24
11 19 0.11
12 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
TATAATTTT
Found at i:57998228 original size:57 final size:55
Alignment explanation
Indices: 57998158--57998284 Score: 123
Period size: 57 Copynumber: 2.2 Consensus size: 55
57998148 TGGTATAATT
** * *
57998158 TTTATAATTTTTTATGAA-ATTTATATTTCTTTACATTTTGTATAATTTTCTTATGA-C
1 TTTATAAAATTTTAT-AATATTTATATTTCTATACA-TTT-TATAATTTT-TTACGATC
* * *
57998215 TTTATAAAATTTTATAATTTTTTTATATTTCTATATATTTTATAATTTTTTACGATT
1 TTTATAAAATTTTATAA--TATTTATATTTCTATACATTTTATAATTTTTTACGATC
57998272 TTTATAAAATTTT
1 TTTATAAAATTTT
57998285 GCAACTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
56 7 0.12
57 35 0.59
58 3 0.05
59 14 0.24
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (55 bp):
TTTATAAAATTTTATAATATTTATATTTCTATACATTTTATAATTTTTTACGATC
Found at i:57998294 original size:57 final size:59
Alignment explanation
Indices: 57998177--57998294 Score: 143
Period size: 57 Copynumber: 2.0 Consensus size: 59
57998167 TTTTATGAAA
* * * *
57998177 TTTATATTTCTTTACATTTTGTATAATTTTCTTATGACTTTATAAAATTTTATAATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAACTTT
* * *
57998236 TTTATATTTCTATATA-TTT-TATAATTTT-TTACGATTTTTATAAAATTTTGCAACTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTACAACTTT
57998293 TT
1 TT
57998295 ATTTTTTTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
56 5 0.10
57 29 0.57
58 3 0.06
59 14 0.27
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (59 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAACTTT
Found at i:57998310 original size:16 final size:17
Alignment explanation
Indices: 57998290--57998327 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
57998280 ATTTTGCAAC
57998290 TTTTTATTTTTTTAC-AA
1 TTTTTATTTTTTT-CTAA
57998307 TTTTTATTTTTTTCTAA
1 TTTTTATTTTTTTCTAA
57998324 TTTT
1 TTTT
57998328 AATAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTTCTAA
Found at i:57998383 original size:29 final size:29
Alignment explanation
Indices: 57998324--57998394 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
57998314 TTTTTTCTAA
* *
57998324 TTTTAATAAATTTT--TAATATTTGAATT
1 TTTTATTAAATTTTAATAATATTTGAATC
57998351 TTTTATTAAATTTTAATAATATTT-ATATC
1 TTTTATTAAATTTTAATAATATTTGA-ATC
*
57998380 TTTTATT-GATTTTAA
1 TTTTATTAAATTTTAA
57998395 GTTTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 13 0.34
28 8 0.21
29 17 0.45
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTATTAAATTTTAATAATATTTGAATC
Found at i:58004830 original size:107 final size:107
Alignment explanation
Indices: 58004657--58004854 Score: 342
Period size: 107 Copynumber: 1.9 Consensus size: 107
58004647 TTTTAAGAGG
* *
58004657 ATATTTGGCTATTTAGTCGAACGAGAAATCAAAACCCAACGCGTTAGGGCACGTTTCCTCGATTT
1 ATATTTGGCTATTTAGTCAAACGAGAAATCAAAACCCAACACGTTAGGGCACGTTTCCTCGATTT
*
58004722 TCCAAACGCGAAGTATTGCCTTATTTTAAAAGTTTAAAAAGA
66 TCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGA
* * *
58004764 ATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTT
1 ATATTTGGCTATTTAGTCAAACGAGAAATCAAAACCCAACACGTTAGGGCACGTTTCCTCGATTT
58004829 TCCAAACGCGAAATATTGCCTTATTT
66 TCCAAACGCGAAATATTGCCTTATTT
58004855 AGAAAAAACT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 85 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (107 bp):
ATATTTGGCTATTTAGTCAAACGAGAAATCAAAACCCAACACGTTAGGGCACGTTTCCTCGATTT
TCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGA
Found at i:58007623 original size:18 final size:18
Alignment explanation
Indices: 58007592--58007644 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
58007582 GCAATATATG
58007592 TAAAAATA-ATTTAAAATA
1 TAAAAATATA-TTAAAATA
* *
58007610 TAAAAATTTATTAATATA
1 TAAAAATATATTAAAATA
*
58007628 TAACAATATATGTAAAA
1 TAAAAATATAT-TAAAA
58007645 ACAATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAATATATTAAAATA
Found at i:58007783 original size:34 final size:35
Alignment explanation
Indices: 58007723--58007789 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
58007713 CAAACACCAG
* *
58007723 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
* *
58007758 AAAACATTTTCCCG-AAATAATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAA
58007790 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
Found at i:58011276 original size:3 final size:3
Alignment explanation
Indices: 58011268--58011322 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
58011258 ATTACTCAAC
* * * * * *
58011268 TAT TAT TAT TAT TAT TGT TAT TAT TAA TGT TAT TAT AAC TAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58011316 TAT TAT T
1 TAT TAT T
58011323 TATATTGGGT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:58017740 original size:13 final size:13
Alignment explanation
Indices: 58017711--58017749 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
58017701 TTATGGAAAA
*
58017711 TATTTTTT-TTAT
1 TATTTTTTATTTT
*
58017723 AATTTTTTATTTT
1 TATTTTTTATTTT
58017736 TATTTTTTATTTT
1 TATTTTTTATTTT
58017749 T
1 T
58017750 TTAACGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:58018181 original size:22 final size:21
Alignment explanation
Indices: 58018142--58018186 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
58018132 ATATAAAAGT
*
58018142 TATTTTATATTGATATTTTATA
1 TATTTTATATTGA-AATTTATA
58018164 TATTTTATAATT-AAATTTATA
1 TATTTTAT-ATTGAAATTTATA
58018185 TA
1 TA
58018187 AAAATATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 9 0.43
23 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTATATTGAAATTTATA
Found at i:58020647 original size:9 final size:9
Alignment explanation
Indices: 58020633--58020717 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
58020623 GTAGTGATTC
58020633 AATTCGGTT
1 AATTCGGTT
58020642 AATTCGGTT
1 AATTCGGTT
58020651 AATTCGGTT
1 AATTCGGTT
*
58020660 AATTCGGGT
1 AATTCGGTT
*
58020669 AATTCGGGT
1 AATTCGGTT
* *
58020678 AATTTGGGT
1 AATTCGGTT
*
58020687 AATTCGATT
1 AATTCGGTT
*
58020696 AATTCAGTT
1 AATTCGGTT
*
58020705 AATTCGATT
1 AATTCGGTT
58020714 AATT
1 AATT
58020718 TAGTTAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:58021975 original size:7 final size:7
Alignment explanation
Indices: 58021963--58021992 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
58021953 CCAACCTTCT
58021963 CCTCTCC
1 CCTCTCC
58021970 CCTCTCC
1 CCTCTCC
58021977 CCTCTCC
1 CCTCTCC
58021984 CCTCTCC
1 CCTCTCC
58021991 CC
1 CC
58021993 CTTCCAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (7 bp):
CCTCTCC
Found at i:58026163 original size:19 final size:19
Alignment explanation
Indices: 58026139--58026185 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
58026129 AACGTCTCTT
*
58026139 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
58026158 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
58026177 TATGCATTA
1 TTTGCATTA
58026186 GATTTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:58028860 original size:10 final size:10
Alignment explanation
Indices: 58028846--58028911 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 10
58028836 TAAAAAATAT
58028846 AAAAAAAGAGG
1 AAAAAAAGA-G
58028857 AAAAAAAGAG
1 AAAAAAAGAG
*
58028867 AAAAAGAAAAAG
1 -AAAA-AAAGAG
58028879 AAAGAAGAAGAG
1 AAA-AA-AAGAG
*
58028891 AAAAGAAAAAAG
1 -AAA-AAAAGAG
58028903 AAAAAAAGA
1 AAAAAAAGA
58028912 AAAGGAGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
10 6 0.13
11 20 0.43
12 14 0.30
13 6 0.13
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:58028877 original size:7 final size:7
Alignment explanation
Indices: 58028858--58028914 Score: 53
Period size: 8 Copynumber: 7.6 Consensus size: 7
58028848 AAAAAGAGGA
58028858 AAAAAAG
1 AAAAAAG
58028865 AGAAAAAG
1 A-AAAAAG
58028873 -AAAAAG
1 AAAAAAG
58028879 AAAGAAGAAG
1 -AA-AA-AAG
*
58028889 AGAAAAG
1 AAAAAAG
58028896 AAAAAAG
1 AAAAAAG
58028903 AAAAAAAG
1 -AAAAAAG
58028911 AAAA
1 AAAA
58028915 GGAGAGGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 6 0.14
7 14 0.33
8 16 0.38
9 3 0.07
10 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:58030101 original size:45 final size:45
Alignment explanation
Indices: 58029977--58031108 Score: 585
Period size: 45 Copynumber: 26.2 Consensus size: 45
58029967 ACAGATCAAT
* * * * * * *
58029977 GAAGATAGCAGATCTTGCCCTCCTGTACTGACAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * * * *
58030022 GAAGATACCAG-CCTTGCCTTCCTGTACTGACAGCGGAGCAGA-C
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
*
58030065 TGAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
1 -GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
*
58030111 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* *
58030156 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
*
58030201 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * * * * * *
58030246 AAAAATAGTAGATCTT-ACTTTTCTGTACTGACAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGTC-TTCCTATATTGGCAGCGAAGTAGATC
* * * * ** *
58030291 AAAGATA-C---TATAGT-TTGC-A-A-T-AAAGC--AG-AC-T-
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* **
58030322 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
*
58030367 GAAGATAGCAGATCTTGTCTTTCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * *
58030412 GAAAATAACAGATCTTATCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * *
58030457 GAAGATAGCAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * ** * *
58030502 GAAGATA-C-CA--TAGT-TTTC-AGTA-AAGCAGACTAA--AGATA
1 GAAGATAGCAGATCTTGTCTTCCTA-TATTGGCAG-CGAAGTAGATC
* * * * * ** ** * *
58030540 GCAGAT--CTTG-CCTT-CCTGTACTGGCA---GCAAAGCAG-AT--C
1 GAAGATAGC-AGATCTTGTCT-TCCT-ATATTGGCAGCGAAGTAGATC
* * * * * *
58030578 GAAGACACCAG-CCTTGTCTTCCTGTATTGACAGCGGAA-CAGA-C
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGC-GAAGTAGATC
* * * * * ** ** *
58030621 TAAAGATAGCAGATCATGCCTTCTTGTACCGATAGCGAAGCAGATC
1 -GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * * * * *
58030667 GAAGACACCAG-CCTTGCCTTCCTGTATTGACAGCGGAGCA-AAC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* *
58030710 TGAAGATAGCAGACCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 -GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * *
58030756 GAAGATAGCAGATCTCGTCTTTCTATATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* *
58030801 GAAGATAGCAGATCTTTTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * *
58030846 GAATATAGCAGATCTTG-CTTTTCTATACTGACAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGTC-TTCCTATATTGGCAGCGAAGTAGATC
* * * ** *
58030891 GAAGATA-C---TATAGT-TTGC-A-A-T-AAAGC--AG-AC-T-
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * *
58030922 GAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * *
58030967 AAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATA
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
* * * * *
58031012 AAAAATAGTAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
** * * ** *
58031057 GAAGATAGCAGATCTTACCTTCCTATACTGACAATGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
58031102 GAAGATA
1 GAAGATA
58031109 CCATAGTTTT
Statistics
Matches: 845, Mismatches: 180, Indels: 124
0.74 0.16 0.11
Matches are distributed among these distances:
31 12 0.01
32 4 0.00
33 2 0.00
34 4 0.00
35 8 0.01
36 12 0.01
37 3 0.00
38 19 0.02
39 16 0.02
40 26 0.03
41 11 0.01
42 8 0.01
43 7 0.01
44 85 0.10
45 624 0.74
46 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
Found at i:58030398 original size:166 final size:166
Alignment explanation
Indices: 58030156--58030463 Score: 483
Period size: 166 Copynumber: 1.9 Consensus size: 166
58030146 GAAGTAGATC
58030156 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCT
1 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCT
* ** *
58030221 TCCTGTATTGGCAGCGAAGTAGATCAAAAATAGTAGATCTTA-CTTTTCTGTACTGACAGTGAAG
66 TCCTATATTGGCAGCGAAGTAGATCAAAAATAACAGATCTTATC-TTCCTGTACTGACAGTGAAG
58030285 CAGATCAAAGATACTATAGTTTGCAATAAAGCAGACT
130 CAGATCAAAGATACTATAGTTTGCAATAAAGCAGACT
* * *
58030322 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGTAGATCGAAGATAGCAGATCTTGTCT
1 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCT
* * * * *
58030387 TTCTATATTGGCAGCGAAGTAGATCGAAAATAACAGATCTTATCTTCCTGTATTGGCAGTGAAGT
66 TCCTATATTGGCAGCGAAGTAGATCAAAAATAACAGATCTTATCTTCCTGTACTGACAGTGAAGC
*
58030452 AGATCGAAGATA
131 AGATCAAAGATA
58030464 GCAGATCTTG
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
166 127 0.99
167 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (166 bp):
GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCT
TCCTATATTGGCAGCGAAGTAGATCAAAAATAACAGATCTTATCTTCCTGTACTGACAGTGAAGC
AGATCAAAGATACTATAGTTTGCAATAAAGCAGACT
Found at i:58030488 original size:211 final size:211
Alignment explanation
Indices: 58030111--58030582 Score: 710
Period size: 211 Copynumber: 2.2 Consensus size: 211
58030101 GAAGTAGATC
* * *
58030111 GAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTCGTCT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTCGTCT
* * *
58030176 TCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
66 TCCTATATTGGCAGCAAAGTAGATCGAAAATAACAGATCTTATCTTCCTGTATTGGCAGCGAAGT
* * * * *
58030241 AGATCAAAAATAGTAGATCTTACTTTTCTGTACTGACAGTGAAGCAGATCAAAGATACTATAGTT
131 AGATCAAAAATAGCAGATCTTACCTTCCTATACTGACAGTGAAGCAGATCAAAGATACCATAGTT
58030306 TGCAATAAAGCAGACT
196 TGCAATAAAGCAGACT
* *
58030322 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGTAGATCGAAGATAGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTCGTCT
* * *
58030387 TTCTATATTGGCAGCGAAGTAGATCGAAAATAACAGATCTTATCTTCCTGTATTGGCAGTGAAGT
66 TCCTATATTGGCAGCAAAGTAGATCGAAAATAACAGATCTTATCTTCCTGTATTGGCAGCGAAGT
* * * *
58030452 AGATCGAAGATAGCAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATCGAAGATACCATAGTT
131 AGATCAAAAATAGCAGATCTTACCTTCCTATACTGACAGTGAAGCAGATCAAAGATACCATAGTT
* *
58030517 TTCAGTAAAGCAGACT
196 TGCAATAAAGCAGACT
* * * *
58030533 AAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAAGA
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGA
58030583 CACCAGCCTT
Statistics
Matches: 234, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
211 234 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (211 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTCGTCT
TCCTATATTGGCAGCAAAGTAGATCGAAAATAACAGATCTTATCTTCCTGTATTGGCAGCGAAGT
AGATCAAAAATAGCAGATCTTACCTTCCTATACTGACAGTGAAGCAGATCAAAGATACCATAGTT
TGCAATAAAGCAGACT
Found at i:58030667 original size:165 final size:166
Alignment explanation
Indices: 58030368--58030676 Score: 381
Period size: 165 Copynumber: 1.9 Consensus size: 166
58030358 AAGTAGATCG
* * * * * * *
58030368 AAGATAGCAGATCTTGTCTTTCTATATTGGCAGCGAAGTAGATCGAAAATAACAGATCTTATCTT
1 AAGATAGCAGATCTTGCCTTCCTATACTGGCAGCAAAGCAGATCGAAAACAACAGACCTTATCTT
* * * * * * *
58030433 CCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAGATCTTGCCTTCCTATACTGACAGTGAAGCA
66 CCTGTATTGACAGGGAAGCAGATCAAAGATAGCAGATCATGCCTTCCTATACCGACAGCGAAGCA
*
58030498 GATCGAAGATACCATAGTTTTCAGTAAAGCAGACTA
131 GATCGAAGACACCATAGTTTTCAGTAAAGCAGACTA
* * * *
58030534 AAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAAGACACCAG-CCTTGTCTT
1 AAGATAGCAGATCTTGCCTTCCTATACTGGCAGCAAAGCAGATCGAAAACAACAGACCTTATCTT
* * *
58030598 CCTGTATTGACAGCGGAA-CAGA-CTAAAGATAGCAGATCATGCCTTCTTGTACCGATAGCGAAG
66 CCTGTATTGACAG-GGAAGCAGATC-AAAGATAGCAGATCATGCCTTCCTATACCGACAGCGAAG
58030661 CAGATCGAAGACACCA
129 CAGATCGAAGACACCA
58030677 GCCTTGCCTT
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
164 1 0.01
165 69 0.58
166 49 0.41
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (166 bp):
AAGATAGCAGATCTTGCCTTCCTATACTGGCAGCAAAGCAGATCGAAAACAACAGACCTTATCTT
CCTGTATTGACAGGGAAGCAGATCAAAGATAGCAGATCATGCCTTCCTATACCGACAGCGAAGCA
GATCGAAGACACCATAGTTTTCAGTAAAGCAGACTA
Found at i:58030678 original size:89 final size:89
Alignment explanation
Indices: 58030527--58030760 Score: 306
Period size: 89 Copynumber: 2.6 Consensus size: 89
58030517 TTCAGTAAAG
* * *
58030527 CAGACTAAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCT
1 CAGACTAAAGATAGCAGATCATGCCTTCCTGTACCGACAGCAAAGCAGATCGAAGACACCAGCCT
*
58030592 TGTCTTCCTGTATTGACAGCGGAA
66 TGCCTTCCTGTATTGACAGCGGAA
* * *
58030616 CAGACTAAAGATAGCAGATCATGCCTTCTTGTACCGATAGCGAAGCAGATCGAAGACACCAGCCT
1 CAGACTAAAGATAGCAGATCATGCCTTCCTGTACCGACAGCAAAGCAGATCGAAGACACCAGCCT
*
58030681 TGCCTTCCTGTATTGACAGCGGAG
66 TGCCTTCCTGTATTGACAGCGGAA
* * * * * ** * * *
58030705 CAAACTGAAGATAGCAGACCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
1 CAGACTAAAGATAGCAGATCATGCCTTCCTGTACCGACAGCAAAGCAGATCGAAGA
58030761 TAGCAGATCT
Statistics
Matches: 126, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 126 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (89 bp):
CAGACTAAAGATAGCAGATCATGCCTTCCTGTACCGACAGCAAAGCAGATCGAAGACACCAGCCT
TGCCTTCCTGTATTGACAGCGGAA
Found at i:58031058 original size:166 final size:166
Alignment explanation
Indices: 58030760--58031063 Score: 421
Period size: 166 Copynumber: 1.8 Consensus size: 166
58030750 TAGATCGAAG
* * *
58030760 ATAGCAGATCTCGTCTTTCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTTTCTTCCT
1 ATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
** * * *
58030825 GTATTGGCAGCGAAGTAGATCGAATATAGCAGATCTTGCTTTTCTATACTGACAGTGAAGCAGAT
66 GTATTGGCAGCGAAGTAGATAAAAAATAGCAGATCTTGCTTTCCTATACTGACAGCGAAGCAGAT
58030890 CGAAGATACTATAGTTTGCAATAAAGCAGACTGAAA
131 CGAAGATACTATAGTTTGCAATAAAGCAGACTGAAA
* * **
58030926 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
* * * * * * *
58030991 GTATTGGTAGCGAAGTAGATAAAAAATAGTAGATCTT-ATCTTCCTGTATTGGCAGCGAAGTAGA
66 GTATTGGCAGCGAAGTAGATAAAAAATAGCAGATCTTGCT-TTCCTATACTGACAGCGAAGCAGA
58031055 TCGAAGATA
130 TCGAAGATA
58031064 GCAGATCTTA
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
165 1 0.01
166 117 0.99
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (166 bp):
ATAGCAGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
GTATTGGCAGCGAAGTAGATAAAAAATAGCAGATCTTGCTTTCCTATACTGACAGCGAAGCAGAT
CGAAGATACTATAGTTTGCAATAAAGCAGACTGAAA
Found at i:58031085 original size:211 final size:211
Alignment explanation
Indices: 58030703--58031182 Score: 710
Period size: 211 Copynumber: 2.3 Consensus size: 211
58030693 TTGACAGCGG
* * *
58030703 AGCAAACTGAAGATAGCAGACCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
1 AGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAGA
* ** * *
58030768 TCTCGTCTTTCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTTTCTTCCTGTATTGGC
66 TCTCGTCTTCCTATATTGGCAGCAAAGTAGATAAAAAATAGCAGATCTTATCTTCCTGTATTGGC
* * * * *
58030833 AGCGAAGTAGATCGAATATAGCAGATCTTGCTTTTCTATACTGACAGTGAAGCAGATCGAAGATA
131 AGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACAATGAAGCAGATCGAAGATA
*
58030898 CTATAGTTTGCAATAA
196 CCATAGTTTGCAATAA
* *
58030914 AGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGA
1 AGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAGA
* * * * *
58030979 TCTTGTCTTCCTGTATTGGTAGCGAAGTAGATAAAAAATAGTAGATCTTATCTTCCTGTATTGGC
66 TCTCGTCTTCCTATATTGGCAGCAAAGTAGATAAAAAATAGCAGATCTTATCTTCCTGTATTGGC
58031044 AGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACAATGAAGCAGATCGAAGATA
131 AGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACAATGAAGCAGATCGAAGATA
* *
58031109 CCATAGTTTTCAGTAA
196 CCATAGTTTGCAATAA
* * *
58031125 AGCAGACTGAAGATAGCAGATCTTGTCTTCCTATACTGGCA-TCAAAGTAGATCGAAGA
1 AGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGT-GAAGTAGATCGAAGA
58031183 CACCAGCCTT
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
210 1 0.00
211 239 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (211 bp):
AGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAGA
TCTCGTCTTCCTATATTGGCAGCAAAGTAGATAAAAAATAGCAGATCTTATCTTCCTGTATTGGC
AGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACAATGAAGCAGATCGAAGATA
CCATAGTTTGCAATAA
Found at i:58031140 original size:600 final size:601
Alignment explanation
Indices: 58030036--58031276 Score: 1975
Period size: 600 Copynumber: 2.1 Consensus size: 601
58030026 ATACCAGCCT
* * * * * *
58030036 TGCCTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAGCAGACCTTGTCTTCCTATATTGGCAG
1 TGCCTTCATGTACTGACAGCGAAGCAGATC-GAAGACACCAGACCTTGCCTTCCTATATTGACAG
* * *
58030100 CGAAGTAGATCGAAGATAGCAGATCTCGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGC
65 CGAAGCAAATCGAAGATAGCAGACCTCGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGC
58030165 AGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATT
130 AGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATT
* *
58030230 GGCAGCGAAGTAGATCAAAAATAGTAGATCTTACTTTTCTGTACTGACAGTGAAGCAGATCAAAG
195 GGCAGCGAAGTAGATCAAAAATAGCAGATCTTACTTTTCTATACTGACAGTGAAGCAGATCAAAG
*
58030295 ATACTATAGTTTGCAATAAAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAA
260 ATACTATAGTTTGCAATAAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAA
* * **
58030360 GTAGATCGAAGATAGCAGATCTTGTCTTTCTATATTGGCAGCGAAGTAGATCGAAAATAACAGAT
325 GTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATAAAAAATAACAGAT
* *
58030425 CTTATCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAGATCTTGCCTTCCTATACTGACA
390 CTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACA
*
58030490 GTGAAGCAGATCGAAGATACCATAGTTTTCAGTAAAGCAGACTAAAGATAGCAGATCTTGCCTTC
455 ATGAAGCAGATCGAAGATACCATAGTTTTCAGTAAAGCAGACTAAAGATAGCAGATCTTGCCTTC
* * * *
58030555 CTGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCTTGTCTTCCTGTATTGACAGCGGAACAGA
520 CTATACTGGCAGCAAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCAGAACAGA
58030620 CTAAAGATAGCAGATCA
585 CTAAAGATAGCAGATCA
* * * *
58030637 TGCCTTCTTGTACCGATAGCGAAGCAGATCGAAGACACCAG-CCTTGCCTTCCTGTATTGACAGC
1 TGCCTTCATGTACTGACAGCGAAGCAGATCGAAGACACCAGACCTTGCCTTCCTATATTGACAGC
* * *
58030701 GGAGCAAA-CTGAAGATAGCAGACCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
66 GAAGCAAATC-GAAGATAGCAGACCTCGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGC
* *
58030765 AGATCTCGTCTTTCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTTTCTTCCTGTATT
130 AGATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATT
* * * *
58030830 GGCAGCGAAGTAGATCGAATATAGCAGATCTTGCTTTTCTATACTGACAGTGAAGCAGATCGAAG
195 GGCAGCGAAGTAGATCAAAAATAGCAGATCTTACTTTTCTATACTGACAGTGAAGCAGATCAAAG
*
58030895 ATACTATAGTTTGCAATAAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAA
260 ATACTATAGTTTGCAATAAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAA
* * **
58030960 GTAGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATAAAAAATAGTAGAT
325 GTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATAAAAAATAACAGAT
58031025 CTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACA
390 CTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACA
* *
58031090 ATGAAGCAGATCGAAGATACCATAGTTTTCAGTAAAGCAGACTGAAGATAGCAGATCTTGTCTTC
455 ATGAAGCAGATCGAAGATACCATAGTTTTCAGTAAAGCAGACTAAAGATAGCAGATCTTGCCTTC
* * *
58031155 CTATACTGGCATCAAAGTAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCAGAGCAGA
520 CTATACTGGCAGCAAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCAGAACAGA
* *
58031220 CTGAAGATAGCAGATCT
585 CTAAAGATAGCAGATCA
* * * *
58031237 TACCTTCATGTACTAACAGTGAAGCAGATTGAAGACACCA
1 TGCCTTCATGTACTGACAGCGAAGCAGATCGAAGACACCA
58031277 TAGTTTGTAG
Statistics
Matches: 584, Mismatches: 54, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
599 1 0.00
600 549 0.94
601 33 0.06
602 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (601 bp):
TGCCTTCATGTACTGACAGCGAAGCAGATCGAAGACACCAGACCTTGCCTTCCTATATTGACAGC
GAAGCAAATCGAAGATAGCAGACCTCGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCA
GATCTCGTCTTCCTATATTGGCAGCAAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
GCAGCGAAGTAGATCAAAAATAGCAGATCTTACTTTTCTATACTGACAGTGAAGCAGATCAAAGA
TACTATAGTTTGCAATAAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAG
TAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATAAAAAATAACAGATC
TTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTACCTTCCTATACTGACAA
TGAAGCAGATCGAAGATACCATAGTTTTCAGTAAAGCAGACTAAAGATAGCAGATCTTGCCTTCC
TATACTGGCAGCAAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCAGAACAGAC
TAAAGATAGCAGATCA
Found at i:58031249 original size:45 final size:45
Alignment explanation
Indices: 58031123--58031271 Score: 140
Period size: 45 Copynumber: 3.3 Consensus size: 45
58031113 AGTTTTCAGT
* * * *
58031123 AAAGCAGACTGAAGATAGCAGATCTTGTCTTCCTATACTGGCATC
1 AAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
* * * *
58031168 AAAGTAGA-TCGAAGACACCAG-CCTTGCCTTCCTGTACTGACAGC
1 AAAGCAGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
* * * * *
58031212 AGAGCAGACTGAAGATAGCAGATCTTACCTTCATGTACTAACAGT
1 AAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
* *
58031257 GAAGCAGATTGAAGA
1 AAAGCAGACTGAAGA
58031272 CACCATAGTT
Statistics
Matches: 81, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
44 34 0.42
45 47 0.58
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (45 bp):
AAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
Found at i:58031591 original size:129 final size:128
Alignment explanation
Indices: 58031432--58031803 Score: 424
Period size: 129 Copynumber: 2.8 Consensus size: 128
58031422 ATCGAAGATG
*
58031432 ACAGATCTTATCTCTCTAAAGTTGCCGTAGAGCAGTTCGCATCCAATCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTCTCT-AAGTTGCAGTAGAGCAGTTCGCATCCAATCTTATCTCCCTGAAGTTG
* * * * * *
58031497 CAGTGGAGTAGATTGAAGTTAGT-AGTCCTATCTCCCTTATGTTGCAGTGAAGTGGATTAAAACC
65 CAGTGGAGTAGATTGAAG-AAATCAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC
*
58031561 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTCTCT-AAGTTGCAGTAGAGCAGTTCGCATCCAATCTTATCTCCCTGAAGTTG
* * **
58031626 CAGTGGAATAGATTGAAGAAATCAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAATG
65 CAGTGGAGTAGATTGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC
* * * * * *
58031690 ACAGATCTTATCTCTCTAATTTTGCAGTAGAGCGGATCACACCATGACAAGTCTTATCTCCCTAA
1 ACAGATCTTATCTCTCTAA-GTTGCAGTAGAGCAG-T-TC-GCAT-CCAA-TCTTATCTCCCTGA
* * * * *
58031755 AGTTGCAGTGGAGCAGACTGGAGATAA-CAAACTTTATCTCCCTGAAGTT
60 AGTTGCAGTGGAGTAGATTGAAGA-AATCAATC-CTATCTCCCTGAAGTT
58031804 AAAATGGAGC
Statistics
Matches: 207, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
128 4 0.02
129 143 0.69
131 1 0.00
132 3 0.01
133 3 0.01
134 37 0.18
135 16 0.08
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (128 bp):
ACAGATCTTATCTCTCTAAGTTGCAGTAGAGCAGTTCGCATCCAATCTTATCTCCCTGAAGTTGC
AGTGGAGTAGATTGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC
Found at i:58031621 original size:41 final size:42
Alignment explanation
Indices: 58031433--58031629 Score: 141
Period size: 41 Copynumber: 4.6 Consensus size: 42
58031423 TCGAAGATGA
* * * * *
58031433 CAGATCTTATCTCTCTAAAGTTGCCGTAGAGCAGTTCGCATC
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATC
* * *
58031475 CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGT-
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAA-TC
* * * * ** ** *
58031516 TAGTAGTCCTATCTCCCTTATGTTGCAGT-GAAGTGGATTAAAACC
1 CAG-A-TCTTATCTCCCTGAAGTTGCAGTAG-AGCAGA-TCGAATC
* *
58031561 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATC
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATC
58031604 CA-ATCTTATCTCCCTGAAGTTGCAGT
1 CAGATCTTATCTCCCTGAAGTTGCAGT
58031630 GGAATAGATT
Statistics
Matches: 118, Mismatches: 28, Indels: 19
0.72 0.17 0.12
Matches are distributed among these distances:
41 53 0.45
42 5 0.04
43 5 0.04
44 48 0.41
45 5 0.04
46 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATC
Found at i:58031795 original size:45 final size:44
Alignment explanation
Indices: 58031476--58031857 Score: 190
Period size: 44 Copynumber: 8.7 Consensus size: 44
58031466 GTTCGCATCC
* * * **
58031476 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACA
* * * * * ** * * *
58031520 AGTCCTATCTCCCTTATGTTGCAGTGAAGTGGA-TTAAAACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-TACA
* * * * *
58031564 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCG--CAT-CC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATACA
** * *
58031605 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGAAATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CA
* * * * * *
58031649 AATCCTATCTTCCTGAAGTTGCAGTGAAGCGGA-TTAAAATGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACA
* * * * * * *
58031693 GATCTTATCTCTCT-AATTTTGCAGTAGAGCGGA-TCACACCATGACA
1 AATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACTGA-A-GAT-ACA
* * *
58031739 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGGAGATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACA
** * * * *
58031784 AA-CTTTATCTCCCTGAAGTTAAAATGGAGCAGATTGAAGCTACT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACA
58031828 AATCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC
58031858 GGATTAAAAT
Statistics
Matches: 249, Mismatches: 73, Indels: 32
0.70 0.21 0.09
Matches are distributed among these distances:
41 30 0.12
42 1 0.00
43 12 0.05
44 133 0.53
45 39 0.16
46 31 0.12
47 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACA
Found at i:58033727 original size:47 final size:48
Alignment explanation
Indices: 58033634--58033742 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 48
58033624 ATATATGTTC
*
58033634 TTTATATTTTATGATTCATATATATACCTATATATATATATATACTT-
1 TTTATATTTTATGATTCATATACATACCTATATATATATATATACTTA
* * *
58033681 TTTATATTTTATGA-T-AGT-TACATACGTATATATGTATATGCTTACTTA
1 TTTATATTTTATGATTCA-TATACATACCTATATATATATAT--ATACTTA
58033729 TATATATATTTTAT
1 T-T-TATATTTTAT
58033743 ATAATAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
45 19 0.37
46 2 0.04
47 19 0.37
48 1 0.02
49 1 0.02
50 10 0.19
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (48 bp):
TTTATATTTTATGATTCATATACATACCTATATATATATATATACTTA
Found at i:58035601 original size:18 final size:19
Alignment explanation
Indices: 58035573--58035618 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
58035563 CATTGACAAA
58035573 TTAACCGAATTAAATCAAT-
1 TTAACC-AATTAAATCAATG
* *
58035592 TTAACCAATTAATTTAATG
1 TTAACCAATTAAATCAATG
58035611 TTAACCAA
1 TTAACCAA
58035619 AGTTTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (19 bp):
TTAACCAATTAAATCAATG
Found at i:58047890 original size:4 final size:4
Alignment explanation
Indices: 58047881--58047906 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
58047871 TGAGTGAAGC
58047881 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
58047907 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:58053875 original size:89 final size:90
Alignment explanation
Indices: 58053773--58053991 Score: 304
Period size: 89 Copynumber: 2.5 Consensus size: 90
58053763 TTAAGGGTGT
*
58053773 AAAAAGCCTTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCT-CATTTT-TTTGCACTCAATTGA
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCTAC-TTTTGTTTGCACTCAATTGA
58053836 GCACTTGAACTTTCAAAATACATAAA
65 GCACTTGAACTTTCAAAATACATAAA
* *
58053862 AAAAAGCCCTCAAACTTCTT-AAAAAAA-TCAATTAAGCCCCTACTTTTGTTTTCACTCAATTGA
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGT-AATTAAGCCCCTACTTTTGTTTGCACTCAATTGA
* * *
58053925 GTACTTGAACTTTCAAAATGCATCAA
65 GCACTTGAACTTTCAAAATACATAAA
* * *
58053951 AAAGA-CCCTCAAACTTTTTCAAGAAAAGCAATTAAGCCCCT
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCT
58053992 GATCTTATTA
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
87 1 0.01
88 36 0.31
89 78 0.68
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (90 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCTACTTTTGTTTGCACTCAATTGAG
CACTTGAACTTTCAAAATACATAAA
Found at i:58054042 original size:19 final size:17
Alignment explanation
Indices: 58054018--58054067 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
58054008 AGAAAAAAAG
58054018 TTATAATAAATAATAAA
1 TTATAATAAATAATAAA
*
58054035 TTTTATAA-AAATTATTAAA
1 --TTATAATAAA-TAATAAA
58054054 TTATAATAAA-AATA
1 TTATAATAAATAATA
58054068 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
18 6 0.22
19 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATAATAAATAATAAA
Found at i:58054082 original size:18 final size:18
Alignment explanation
Indices: 58054061--58054095 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58054051 AAATTATAAT
58054061 AAAAATATAAAAAATTAA
1 AAAAATATAAAAAATTAA
* *
58054079 AAAATTATTAAAAATTA
1 AAAAATATAAAAAATTA
58054096 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAAAATTAA
Found at i:58054088 original size:11 final size:10
Alignment explanation
Indices: 58054040--58054096 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 10
58054030 ATAAATTTTA
58054040 TAAAAATTAT
1 TAAAAATTAT
58054050 T--AAATTAT
1 TAAAAATTAT
58054058 AATAAAAA-TAT
1 --TAAAAATTAT
*
58054069 AAAAAATTA-
1 TAAAAATTAT
58054078 -AAAAATTAT
1 TAAAAATTAT
58054087 TAAAAATTAT
1 TAAAAATTAT
58054097 AATTTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
8 15 0.38
9 5 0.13
10 13 0.33
11 3 0.08
12 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:58054337 original size:29 final size:28
Alignment explanation
Indices: 58054303--58054402 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 28
58054293 GTACAATAAT
58054303 TTTTATAATTTTTTTACGACTTTATAAAA
1 TTTTATAATTTTTTTACGA-TTTATAAAA
* * *
58054332 TTTTATAAATTTTTTTA-TATTTCTATATA
1 TTTTAT-AATTTTTTTACGATTTATA-AAA
58054361 TTTTATAA-TTTTTTACGATTTTTATAAAA
1 TTTTATAATTTTTTTACGA--TTTATAAAA
*
58054390 TTTTACAATTTTT
1 TTTTATAATTTTT
58054403 GTTCTAATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
27 7 0.12
28 8 0.14
29 24 0.41
30 19 0.33
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTATAATTTTTTTACGATTTATAAAA
Found at i:58054383 original size:19 final size:19
Alignment explanation
Indices: 58054361--58054402 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
58054351 TTTCTATATA
** *
58054361 TTTTATAATTTTTTACGAT
1 TTTTATAAAATTTTACAAT
58054380 TTTTATAAAATTTTACAAT
1 TTTTATAAAATTTTACAAT
58054399 TTTT
1 TTTT
58054403 GTTCTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAAAATTTTACAAT
Found at i:58060182 original size:26 final size:26
Alignment explanation
Indices: 58060153--58060214 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
58060143 CCTGTAAGTG
58060153 TTCTGAAACTGAAACATACTATGATA
1 TTCTGAAACTGAAACATACTATGATA
* * **
58060179 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGAAACATACTATGATA
*
58060205 TACTGAAACT
1 TTCTGAAACT
58060215 ACTATAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (26 bp):
TTCTGAAACTGAAACATACTATGATA
Found at i:58065694 original size:34 final size:34
Alignment explanation
Indices: 58065651--58065718 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
58065641 ACATTTTTGA
* *
58065651 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
*
58065684 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAGACTGT
58065719 TTAACTATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:58071528 original size:38 final size:39
Alignment explanation
Indices: 58071444--58071529 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 39
58071434 CACTTTACAT
* * *
58071444 GCCAGGATTCACTTAGTGTGCCAGATATGCACTCCATGT
1 GCCAGGATGCACATAGTGTGCCAGATATGCACTCCATGC
* * ***
58071483 GCTAGGATGCACATAGTGTGCTA-ATATGCACTTTGTGC
1 GCCAGGATGCACATAGTGTGCCAGATATGCACTCCATGC
58071521 GCCAGGATG
1 GCCAGGATG
58071530 TGTTCTGTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
38 19 0.50
39 19 0.50
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (39 bp):
GCCAGGATGCACATAGTGTGCCAGATATGCACTCCATGC
Found at i:58072618 original size:31 final size:31
Alignment explanation
Indices: 58072583--58072646 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
58072573 ACTACCATAC
58072583 TTAACGTATCAACTCTCACTTCACACCTTAG
1 TTAACGTATCAACTCTCACTTCACACCTTAG
58072614 TTAACGTATCAACTCTCACTTCACACCTTAG
1 TTAACGTATCAACTCTCACTTCACACCTTAG
58072645 TT
1 TT
58072647 GACTCCAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (31 bp):
TTAACGTATCAACTCTCACTTCACACCTTAG
Found at i:58075528 original size:26 final size:26
Alignment explanation
Indices: 58075499--58075571 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
58075489 TCTCATCCCT
58075499 ATTTTACCCAC-AACAAAATTTTGATG
1 ATTTTACCC-CTAACAAAATTTTGATG
** *
58075525 ATTTTACCCCTAGTAAACTTTTGATG
1 ATTTTACCCCTAACAAAATTTTGATG
* *
58075551 ATTTTTCCCCTAATAAAATTT
1 ATTTTACCCCTAACAAAATTT
58075572 CAAGAAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATTTTGATG
Found at i:58083852 original size:24 final size:25
Alignment explanation
Indices: 58083800--58083846 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
58083790 TTACCCTCTC
* *
58083800 GAGCTTCCCGTTATATGGTTCTTGT
1 GAGCTTCCCGTTATATAGCTCTTGT
58083825 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
58083847 TGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGT
Found at i:58084452 original size:73 final size:73
Alignment explanation
Indices: 58084331--58084472 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 73
58084321 CTCAGATTTT
** * * *
58084331 AAAAAAAGGGGTCATGCCCAGTAAGTTAGGGCACAATCTTTTCTTAATTCCCGAGATCGTTTAAA
1 AAAAAAAGGGACCATGCCCAGTAAGTTAGGACACAATCTTTTCGTAATTCCCAAGATCGTTTAAA
58084396 ACTTGAGA
66 ACTTGAGA
* *
58084404 AAAAAAAGGGACCATGCCCAGTAAGTTAGGACACGATCTTTTCGTAATTCCTAAGATCGTTTAAA
1 AAAAAAAGGGACCATGCCCAGTAAGTTAGGACACAATCTTTTCGTAATTCCCAAGATCGTTTAAA
58084469 ACTT
66 ACTT
58084473 AAGTTTGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (73 bp):
AAAAAAAGGGACCATGCCCAGTAAGTTAGGACACAATCTTTTCGTAATTCCCAAGATCGTTTAAA
ACTTGAGA
Found at i:58084902 original size:29 final size:29
Alignment explanation
Indices: 58084845--58084902 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
58084835 AAAAAGGTAT
*
58084845 ATATGTATGTATATAGATATAAATTAAAA
1 ATATGTATGTATATAGATATAAATCAAAA
* *
58084874 ATATGTATGTATGTATATATATAA-CAAAA
1 ATATGTATGTATATAGATATA-AATCAAAA
58084903 TTTGAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (29 bp):
ATATGTATGTATATAGATATAAATCAAAA
Found at i:58084956 original size:22 final size:21
Alignment explanation
Indices: 58084927--58084967 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
58084917 GACATAGATG
58084927 AATAAATAACAATAATAATGT
1 AATAAATAACAATAATAATGT
**
58084948 AATATAATAGTAATAATAAT
1 AATA-AATAACAATAATAAT
58084968 ATTAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
AATAAATAACAATAATAATGT
Found at i:58086477 original size:44 final size:44
Alignment explanation
Indices: 58086427--58086570 Score: 207
Period size: 44 Copynumber: 3.3 Consensus size: 44
58086417 GTGATACGAT
58086427 TTGTAGCTTCAATCCACTCTGCTGCAACTTCAGGGAGATATGAG
1 TTGTAGCTTCAATCCACTCTGCTGCAACTTCAGGGAGATATGAG
*
58086471 TTGTAGCTTCAATCCCCTCTGCTGCAACTTCAGGGAGATATGAG
1 TTGTAGCTTCAATCCACTCTGCTGCAACTTCAGGGAGATATGAG
* ** ** * *
58086515 TTGTAGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
1 TTGTAGCTTCAATCCACTCTGCTGCAACTTCAGGGAGATATGAG
*
58086559 TTGTATCTTCAA
1 TTGTAGCTTCAA
58086571 CCTGCCCCAC
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
TTGTAGCTTCAATCCACTCTGCTGCAACTTCAGGGAGATATGAG
Found at i:58086581 original size:44 final size:43
Alignment explanation
Indices: 58086448--58086790 Score: 310
Period size: 44 Copynumber: 7.6 Consensus size: 43
58086438 ATCCACTCTG
* * ** **
58086448 CTGCAACTTCAGGGAGATATGAGTTGTAGCTTCAATCCCCTCTG
1 CTGCAACTTCAGGGAGATAAGA-TTGTATCTTCAATCTGCTCCA
* * *
58086492 CTGCAACTTCAGGGAGATATGAGTTGTAGCTTCAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGA-TTGTATCTTCAATCTGCTCCA
* *
58086536 CTGCAACTTCAGGGAGATAAGACTTGTATCTTCAACCTGCCCCA
1 CTGCAACTTCAGGGAGATAAGA-TTGTATCTTCAATCTGCTCCA
* * *
58086580 CTGCAACTTCAGAGAGATAAGATTGGTAGTTTATAGCTTTAATCTGTTCCA
1 CTGCAACTTCAGGGAGATAAGA-T--T-G--TAT--CTTCAATCTGCTCCA
* * *
58086631 CTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGA-TTG-TATCTTCAATCTGCTCCA
* * * *
58086676 CTGCAACTTCAGGGGGGTAGGATTAGTAACTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-GTATCTTCAATCTGCTCCA
* * *
58086720 CTGAAACTTCAGGGAGATAAGATTGGTTTAC-TCAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-GTAT-CTTCAATCTGCTCCA
58086764 CTGCAACTTCAGGGAGATAAGACTTGT
1 CTGCAACTTCAGGGAGATAAGA-TTGT
58086791 TGACTATGAT
Statistics
Matches: 251, Mismatches: 38, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
44 173 0.69
45 35 0.14
46 1 0.00
47 4 0.02
48 1 0.00
49 4 0.02
51 33 0.13
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTGCAACTTCAGGGAGATAAGATTGTATCTTCAATCTGCTCCA
Found at i:58086709 original size:140 final size:139
Alignment explanation
Indices: 58086492--58086746 Score: 368
Period size: 140 Copynumber: 1.8 Consensus size: 139
58086482 ATCCCCTCTG
* *
58086492 CTGCAACTTCAGGGAGATATGAGTTGTAGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGGAAATAAGAGTTGTAGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
58086557 ACTTGTATCTTCAACCTGCCCCACTGCAACTTCAGAGAGATAAGATTGGTAGTTTATAGCTTTAA
66 ACTTGTAACTTCAACCTGCCCCACTGAAACTTCAGAGAGATAAGATTGGTAGTTTATAGCTTTAA
58086622 TCTGTTCCA
131 TCTGTTCCA
* * * * * *
58086631 CTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGGGGTAG
1 CTGCAACTTCAGGGAAATAAGAGTTG-TAGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * *
58086696 GA-TTAGTAACTTCAATCTGCTCCACTGAAACTTCAGGGAGATAAGATTGGT
65 GACTT-GTAACTTCAACCTGCCCCACTGAAACTTCAGAGAGATAAGATTGGT
58086747 TTACTCAGTC
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
139 25 0.25
140 76 0.75
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (139 bp):
CTGCAACTTCAGGGAAATAAGAGTTGTAGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTTGTAACTTCAACCTGCCCCACTGAAACTTCAGAGAGATAAGATTGGTAGTTTATAGCTTTAA
TCTGTTCCA
Found at i:58086905 original size:50 final size:50
Alignment explanation
Indices: 58086830--58087212 Score: 327
Period size: 50 Copynumber: 7.7 Consensus size: 50
58086820 TGCAATGTCG
* * * * * *
58086830 GGGAAGCAAGATTCACCGTTATAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** * *
58086880 GGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTTTTTAACTGCAATGTC-
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* ** * * *
58086929 GAGGAAGCAAGATTCGCCATTGTGGCTTCAATCTGTTCCATTGCACGGCCA
1 G-GGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* ** * * *
58086980 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * * * *
58087030 GGGAAGTAAGATTTGCCGTTGTGGCTTCAATCTGTTCCATTACACTGCCA
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** * * *
58087080 CGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * * * * * **
58087130 GGGAAGCAAGATTCACCGTTGTGGCTTCAATATGTTCCACTACACCACCA
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** *
58087180 ATGAAGTAAGATTCGCTGTTGTAACTTCAATCT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
58087213 ACTTCACTTC
Statistics
Matches: 249, Mismatches: 82, Indels: 4
0.74 0.24 0.01
Matches are distributed among these distances:
49 1 0.00
50 247 0.99
51 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
Found at i:58086938 original size:100 final size:100
Alignment explanation
Indices: 58086814--58087212 Score: 618
Period size: 100 Copynumber: 4.0 Consensus size: 100
58086804 TTTAATTCTA
* *
58086814 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTATAGCTTCAATCTGTTCCACTACACCGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTACACCGCC
*
58086879 AGGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTT
66 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
* * * * * *
58086914 TTTAACTGCAATGTCGAGGAAGCAAGATTCGCCATTGTGGCTTCAATCTGTTCCATTGCACGGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTACACCGCC
58086979 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
66 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
* ** * *
58087014 TTTAACTGCAATGTCGGGGAAGTAAGATTTGCCGTTGTGGCTTCAATCTGTTCCATTACACTGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTACACCGCC
*
58087079 ACGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
66 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
* *
58087114 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATATGTTCCACTACACCACC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTACACCGCC
** *
58087179 AATGAAGTAAGATTCGCTGTTGTAACTTCAATCT
66 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
58087213 ACTTCACTTC
Statistics
Matches: 273, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 273 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (100 bp):
TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTACACCGCC
AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT
Found at i:58087833 original size:38 final size:38
Alignment explanation
Indices: 58087782--58087854 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
58087772 TAACGCCTTC
58087782 TTGCCCGGCTGGCATCTCCAAAGAAACACTTAATCAGA
1 TTGCCCGGCTGGCATCTCCAAAGAAACACTTAATCAGA
* *
58087820 TTGCCCTGCTGGCATCTCCAAAGAAACATTTAATC
1 TTGCCCGGCTGGCATCTCCAAAGAAACACTTAATC
58087855 CCGATTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (38 bp):
TTGCCCGGCTGGCATCTCCAAAGAAACACTTAATCAGA
Found at i:58087950 original size:24 final size:23
Alignment explanation
Indices: 58087873--58087951 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 23
58087863 AGGCTCTTTG
58087873 TGAGCTTCCCGATA-TGGCTCGCT
1 TGAGCTTCCCGATATTGGCTC-CT
* *
58087896 TGAACTTCCCGATATATGGCT-AT
1 TGAGCTTCCCGATAT-TGGCTCCT
*
58087919 CTGAAGCTTCCCGTTATTGGCTCCT
1 -TG-AGCTTCCCGATATTGGCTCCT
58087944 ATGAGCTT
1 -TGAGCTT
58087952 TTTGATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 14 0.31
24 12 0.27
25 19 0.42
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.34
Consensus pattern (23 bp):
TGAGCTTCCCGATATTGGCTCCT
Found at i:58087963 original size:24 final size:23
Alignment explanation
Indices: 58087936--58087983 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
58087926 TTCCCGTTAT
*
58087936 TGGCTCCTATGAGCTTTTTGATTA
1 TGGCTCCTATGAG-TTTTTCATTA
**
58087960 TGGCTTTTATGAGTTTTTCATTA
1 TGGCTCCTATGAGTTTTTCATTA
58087983 T
1 T
58087984 ACAACCTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (23 bp):
TGGCTCCTATGAGTTTTTCATTA
Found at i:58088047 original size:25 final size:26
Alignment explanation
Indices: 58087996--58088067 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
58087986 AACCTTGATA
* *
58087996 AGCTTTCCGTTACATGGCTC-ATATG
1 AGCTTCCCGTTATATGGCTCGATATG
*
58088021 AGCTTCCCGTTATATGGCTCGA-GTG
1 AGCTTCCCGTTATATGGCTCGATATG
58088046 AGGCTTCCCGTT-TATGTGCTCG
1 A-GCTTCCCGTTATATG-GCTCG
58088068 TACAAGCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 25 0.61
26 16 0.39
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (26 bp):
AGCTTCCCGTTATATGGCTCGATATG
Found at i:58088673 original size:14 final size:14
Alignment explanation
Indices: 58088654--58088683 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
58088644 CATTCTTTAG
58088654 AATATTTCCATGTT
1 AATATTTCCATGTT
58088668 AATATTTCCATGTT
1 AATATTTCCATGTT
58088682 AA
1 AA
58088684 CTTTGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (14 bp):
AATATTTCCATGTT
Found at i:58090506 original size:16 final size:17
Alignment explanation
Indices: 58090464--58090507 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
58090454 AAAATAACTT
58090464 TAAAATAATAAACACAAA
1 TAAAATAA-AAACACAAA
58090482 TAAAATAAAAAC-CAAA
1 TAAAATAAAAACACAAA
58090498 -AAAACTAAAA
1 TAAAA-TAAAA
58090508 TAAGTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 4 0.16
18 8 0.32
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (17 bp):
TAAAATAAAAACACAAA
Found at i:58090556 original size:19 final size:19
Alignment explanation
Indices: 58090514--58090556 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
58090504 AAAATAAGTC
* *
58090514 AAAATTAAAAGCAAAAATT
1 AAAATTAAAACCAAAAACT
* *
58090533 GAAATTAAAACCAAAACCT
1 AAAATTAAAACCAAAAACT
58090552 AAAAT
1 AAAAT
58090557 GTGAAATAAG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATTAAAACCAAAAACT
Found at i:58094491 original size:2 final size:2
Alignment explanation
Indices: 58094486--58094518 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
58094476 AAAAAAAAAA
58094486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58094519 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58098625 original size:5 final size:5
Alignment explanation
Indices: 58098615--58098668 Score: 108
Period size: 5 Copynumber: 10.8 Consensus size: 5
58098605 TTAATAATGT
58098615 TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA
1 TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA
58098665 TACT
1 TACT
58098669 TGAGTTTACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
TACTA
Found at i:58100207 original size:22 final size:22
Alignment explanation
Indices: 58100181--58100225 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
58100171 ATATTATAAC
58100181 TTTTTTTATTTACCAAAAAATA
1 TTTTTTTATTTACCAAAAAATA
*
58100203 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAAAATA
58100225 T
1 T
58100226 CAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAAAATA
Found at i:58100335 original size:27 final size:27
Alignment explanation
Indices: 58100297--58100363 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
58100287 CGCCAATGGG
58100297 ATTGGCGGCACCAAAGGTGCCTAA-ACC
1 ATTGGCGGCACCAAAGGTGCC-AATACC
*
58100324 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAATACC
58100351 ATTGGCGGCACCA
1 ATTGGCGGCACCA
58100364 GTGTATATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAATACC
Found at i:58100419 original size:4 final size:4
Alignment explanation
Indices: 58100410--58100556 Score: 126
Period size: 4 Copynumber: 36.0 Consensus size: 4
58100400 GAAGGAGAGG
*
58100410 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * *
58100460 G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
*
58100508 G-AA G-AA GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA
1 GAAA GAAA G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
58100553 GAAA
1 GAAA
58100557 ATGAAATGAG
Statistics
Matches: 120, Mismatches: 10, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
3 15 0.12
4 76 0.63
5 24 0.20
6 5 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:58100476 original size:40 final size:40
Alignment explanation
Indices: 58100401--58100600 Score: 211
Period size: 40 Copynumber: 5.0 Consensus size: 40
58100391 GGGGGACCAG
* *
58100401 AAGGAGAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA
1 AAGGAGA-GGAAAGAAAGAAAGAAAGAAGGAAAG-AA-AAGGA
58100444 AAGGAGAGGAAAGAAAG-AA-AAAGAAGGAAAGAAAAGGA
1 AAGGAGAGGAAAGAAAGAAAGAAAGAAGGAAAGAAAAGGA
*
58100482 AAGGAGAAGAGAAAAAAAGAAAGAAAGAA-G-AAGAAAAGGA
1 AAGGAG-AG-GAAAGAAAGAAAGAAAGAAGGAAAGAAAAGGA
* *
58100522 AAGGAGAAGAAA-AAAGAAAGAAAGAAGGAAAGAAAATGA
1 AAGGAGAGGAAAGAAAGAAAGAAAGAAGGAAAGAAAAGGA
*
58100561 AATGAGAAGAGAAA-AAA-AAAG-AAGAA-GAAGAGAAAAGGA
1 AAGGAG-AG-GAAAGAAAGAAAGAAAGAAGGAA-AGAAAAGGA
58100600 A
1 A
58100601 GGAAAAAAAG
Statistics
Matches: 140, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
37 14 0.10
38 18 0.13
39 33 0.24
40 40 0.29
41 12 0.09
42 16 0.11
43 7 0.05
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (40 bp):
AAGGAGAGGAAAGAAAGAAAGAAAGAAGGAAAGAAAAGGA
Found at i:58100540 original size:45 final size:45
Alignment explanation
Indices: 58100453--58100555 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
58100443 AAAGGAGAGG
* * *
58100453 AAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAGAAAAGAAAAGGAAAGGAAAAAAGAAAA
* *
58100497 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAA-GAAAAAAGAAAG
1 AAAGAAAGAAAGAAGAAGAAAAGAAAAGGA-AAGGAAAAAAGAAAA
*
58100542 AAAGAAGGAAAGAA
1 AAAGAAAGAAAGAA
58100556 AATGAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 11 0.22
45 38 0.75
46 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (45 bp):
AAAGAAAGAAAGAAGAAGAAAAGAAAAGGAAAGGAAAAAAGAAAA
Found at i:58100589 original size:34 final size:36
Alignment explanation
Indices: 58100413--58100600 Score: 166
Period size: 39 Copynumber: 4.9 Consensus size: 36
58100403 GGAGAGGGAA
*
58100413 AGAA-AGAAAGAAAGAAAGAAAGAAAG-AAA-GAAAGG
1 AGAAGAGAAA-AAA-AAAGAAGGAAAGAAAAGGAAAGG
* *
58100448 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGA--AGAGAAAAAAAAAGAAGGAAAGAAAAGGAAAGG
*
58100486 AGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGG
1 AGAAGAG-AAAAAA-AAAG-AAGGA-AAGAAAAGGAAAGG
* * *
58100526 AGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAATGAAATG
1 AGAAG-AGAAA-AAA-AAAGAAGGAAAGAAAAGGAAAGG
58100565 AGAAGAGAAAAAAAAAGAAGAAGAAGAGAAAAGGAA
1 AGAAGAGAAAAAAAAAGAAG--GAA-AGAAAAGGAA
58100601 GGAAAAAAAG
Statistics
Matches: 128, Mismatches: 11, Indels: 24
0.79 0.07 0.15
Matches are distributed among these distances:
35 3 0.02
36 21 0.16
37 14 0.11
38 25 0.20
39 30 0.23
40 26 0.20
41 9 0.07
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (36 bp):
AGAAGAGAAAAAAAAAGAAGGAAAGAAAAGGAAAGG
Found at i:58101374 original size:74 final size:75
Alignment explanation
Indices: 58101244--58101385 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 75
58101234 GTTTATTTCG
*
58101244 GGGTTTTTACCAAAATATTACAAAAAATAAAAAAATACGAAAATATTATAAATTTTTTTTATTTA
1 GGGTTTTTACCAAAATATTACAAAAAATAAAAAAATACCAAAATATTATAAATTTTTTTTATTTA
58101309 CCAGAATAAT
66 CCAGAATAAT
* * *
58101319 GGGTTTTTA-CAAATATATTA-AAAAAAT-TAAAAATAACCAAAATGTTATAAGTTTTTTTTATT
1 GGGTTTTTACCAAA-ATATTACAAAAAATAAAAAAAT-ACCAAAATATTATAAATTTTTTTTATT
58101381 TACCA
64 TACCA
58101386 AAAAATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
73 6 0.10
74 40 0.66
75 15 0.25
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (75 bp):
GGGTTTTTACCAAAATATTACAAAAAATAAAAAAATACCAAAATATTATAAATTTTTTTTATTTA
CCAGAATAAT
Found at i:58101404 original size:25 final size:25
Alignment explanation
Indices: 58101370--58101419 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
58101360 ATGTTATAAG
58101370 TTTTTTTTATTTACCAAAAAATATA
1 TTTTTTTTATTTACCAAAAAATATA
* *
58101395 TTTTTTTTATTTATCAAAATATATA
1 TTTTTTTTATTTACCAAAAAATATA
58101420 AAAAAAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTTTTATTTACCAAAAAATATA
Found at i:58106796 original size:36 final size:36
Alignment explanation
Indices: 58106748--58106858 Score: 102
Period size: 26 Copynumber: 3.4 Consensus size: 36
58106738 ACTCTAAATA
*
58106748 ATACACAAAATAATACACACTAAAATTATTAATTTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
*
58106784 ATACTC--AA-AAT--A-A-T---ATTAATAATTTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
*
58106810 GTACTCAAAATAATACACACTAAAATTATTAA-TTT
1 ATACTCAAAATAATACACACTAAAATTATTAATTTT
*
58106845 -TACTAAAAATAATA
1 ATACTCAAAATAATA
58106859 ACTAACTAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
26 16 0.27
28 2 0.03
29 4 0.07
30 1 0.02
31 2 0.03
32 1 0.02
33 4 0.07
34 15 0.25
35 3 0.05
36 12 0.20
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (36 bp):
ATACTCAAAATAATACACACTAAAATTATTAATTTT
Found at i:58107002 original size:3 final size:3
Alignment explanation
Indices: 58106994--58107037 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58106984 TTAATACATT
58106994 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
58107038 TAATAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:58107042 original size:3 final size:3
Alignment explanation
Indices: 58107036--58107090 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
58107026 CAACAACAAC
*
58107036 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58107084 AAT AAT A
1 AAT AAT A
58107091 CATTTTGAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58107160 original size:19 final size:21
Alignment explanation
Indices: 58107136--58107174 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
58107126 AAACAAAAAA
*
58107136 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
58107155 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
58107175 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:58107225 original size:21 final size:20
Alignment explanation
Indices: 58107200--58107238 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
58107190 AAAAATACCT
*
58107200 TCTTTTTCTCCTTTTTTTCTC
1 TCTTTTTCT-CTTCTTTTCTC
58107221 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
58107239 CGCAGCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:58107238 original size:10 final size:11
Alignment explanation
Indices: 58107198--58107237 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
58107188 TTAAAAATAC
58107198 CTTCTTTTTCT
1 CTTCTTTTTCT
58107209 CCTT-TTTTTCT
1 -CTTCTTTTTCT
58107220 C-TCTTTTTCT
1 CTTCTTTTTCT
58107230 CTTCTTTT
1 CTTCTTTT
58107238 CCGCAGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 9 0.35
11 13 0.50
12 3 0.12
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:58107368 original size:27 final size:27
Alignment explanation
Indices: 58107338--58107392 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
58107328 ATTAGTATGA
**
58107338 CACCATTGGTGCCGCCAATGGCATTGG
1 CACCATTGGTGCCGCCAATCCCATTGG
58107365 CACCATTGGTGCCGCCAATCCCATTGG
1 CACCATTGGTGCCGCCAATCCCATTGG
58107392 C
1 C
58107393 GTGACCAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (27 bp):
CACCATTGGTGCCGCCAATCCCATTGG
Found at i:58107483 original size:21 final size:19
Alignment explanation
Indices: 58107442--58107480 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
58107432 TTTTTTTGAT
58107442 ATATTTTGGTAAATAAAAA
1 ATATTTTGGTAAATAAAAA
58107461 ATATTTTGGTAAATAAAAA
1 ATATTTTGGTAAATAAAAA
58107480 A
1 A
58107481 AATTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
ATATTTTGGTAAATAAAAA
Found at i:58110757 original size:11 final size:11
Alignment explanation
Indices: 58110741--58110765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58110731 GGCATGATGA
58110741 TTTTTTGTTTT
1 TTTTTTGTTTT
58110752 TTTTTTGTTTT
1 TTTTTTGTTTT
58110763 TTT
1 TTT
58110766 ATAAAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:58120378 original size:19 final size:19
Alignment explanation
Indices: 58120356--58120393 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
58120346 AAAAAATCGA
58120356 GAAACTTGAAAAATTCATC
1 GAAACTTGAAAAATTCATC
58120375 GAAACTTGAAAAATTCATC
1 GAAACTTGAAAAATTCATC
58120394 TGATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
GAAACTTGAAAAATTCATC
Found at i:58135760 original size:121 final size:121
Alignment explanation
Indices: 58135533--58135774 Score: 385
Period size: 121 Copynumber: 2.0 Consensus size: 121
58135523 GAGATTAACA
* * *
58135533 GCTAATAGGCAGTGCCTGTTTAAAGGGCCAAAGAGGAAAGACCGATGTTTTGGCATAGCATGCCT
1 GCTAAAAGGCAGTGCCTGTTTAAAAGGCCAAAGAGGAAAGACCGATGTTTTGGCATAGCATACCT
58135598 ACTGTTATGATCTATTAATTTCAAATACCCCAGCTTATTACTCACCTGTGTCGCCT
66 ACTGTTATGATCTATTAATTTCAAATACCCCAGCTTATTACTCACCTGTGTCGCCT
* * *
58135654 GCTAAAAGGCAGTGCCTGTTTAAAAGGCCAAAGAGGAGAGGCCGATGTTTTGGCATAGCATACTT
1 GCTAAAAGGCAGTGCCTGTTTAAAAGGCCAAAGAGGAAAGACCGATGTTTTGGCATAGCATACCT
* ** * *
58135719 GCTGTTATGATCTATTAATTTCAAATATTCCGGCTTCTTACTCACCTGTGTCGCCT
66 ACTGTTATGATCTATTAATTTCAAATACCCCAGCTTATTACTCACCTGTGTCGCCT
58135775 TGGTATCAGA
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 110 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (121 bp):
GCTAAAAGGCAGTGCCTGTTTAAAAGGCCAAAGAGGAAAGACCGATGTTTTGGCATAGCATACCT
ACTGTTATGATCTATTAATTTCAAATACCCCAGCTTATTACTCACCTGTGTCGCCT
Found at i:58138335 original size:30 final size:31
Alignment explanation
Indices: 58138301--58138361 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
58138291 AAACCTTTTT
* *
58138301 ACTTTTCCCTCAAAACTTTTACTC-CTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
*
58138331 ACTTTCCCCCCAAAACTTTTATTCTCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
58138362 CTCCCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
Found at i:58138883 original size:17 final size:17
Alignment explanation
Indices: 58138829--58138909 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
58138819 TTATTTCTAC
58138829 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
58138846 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
58138865 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
*
58138882 TATTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
58138899 TATTTATATTA
1 TATTTATATTA
58138910 AAATTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 7 0.13
19 11 0.21
20 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:58139256 original size:5 final size:5
Alignment explanation
Indices: 58139246--58139271 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58139236 GAACAAATAT
58139246 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
58139272 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Done.